DESCRIPTION

The molecule program draws several different representations of
molecules. Some common molecules are built in, and it can read PDB
(Protein Data Base) files as input.

OPTIONS

molecule
accepts the following options:

-window

Draw on a newly-created window. This is the default.

-root

Draw on the root window.

-install

Install a private colormap for the window.

-visual visual

Specify which visual to use. Legal values are the name of a visual class,
or the id number (decimal or hex) of a specific visual.

-fps

Display a running tally of how many frames per second are being rendered.
In conjunction with -delay 0, this can be a useful benchmark of
your GL performance.

-wander

Move the molecules around the screen.

-no-wander

Keep the molecule centered on the screen. This is the default.

-spin

Which axes around which the molecule should spin. The default is "XYZ",
meaning rotate it freely in space. "-spin Z" would rotate the
molecule in the plane of the screen while not rotating it into or out
of the screen; etc.

-no-spin

Don't spin it at all: the same as -spin "".

-labels

Draw labels on the atoms (or the spot where the atoms would be.)
This is the default.

-no-labels

Do not draw labels on the atoms.

-titles

Print the name of the molecule and its chemical formula at the top of
the screen.

-no-titles

Do not print the molecule name.

-atoms

Represent the atoms as shaded spheres of appropriate sizes.
This is the default.

-no-atoms

Do not draw spheres for the atoms: only draw bond lines.

-bonds

Represent the atomic bonds as solid tubes of appropriate thicknesses.
This is the default.

-no-bonds

Do not draw the bonds: instead, make the spheres for the atoms be
larger, for a "space-filling" representation of the molecule.

-wire

Draw a wireframe rendition of the molecule: this will consist only of
single-pixel lines for the bonds, and text labels where the atoms go.
This will be very fast.

-timeout seconds

When using the built-in data set, change to a new molecule every
this-many seconds. Default is 20 seconds.

-molecule filename

Instead of using the built-in molecules, read one from the given file.
This file must be in PDB (Protein Data Base) format. (Note that it's
not uncommon for PDB files to contain only the atoms, with no (or
little) information about the atomic bonds.)

When the molecule is too large (bigger than about 30 angstroms from
side to side), the -label option will be automatically turned
off, because otherwise, the labels would overlap and completely obscure
the display.

When the molecule is around 150 angstroms from side to side, wireframe
mode will be turned on (because otherwise it would be too slow.)

ENVIRONMENT

DISPLAY

to get the default host and display number.

XENVIRONMENT

to get the name of a resource file that overrides the global resources
stored in the RESOURCE_MANAGER property.